Create figures for CyTOF myeloid panel data. Preprocessing and preliminary analysis were done by Dimitrios N. Sidiropoulos.
##
## Baseline C1D1 C2D1
## 28 28 8
## The number of paired samples between Baseline and C1D1: 28
## The number of paired samples between Baseline and C2D1: 8
## The number of paired samples between C2D1 and C1D1: 8
P-values from paired two-sided Wilcoxon test between time points and mean of difference between time points
| pValue_BvsC1D1 | mean(C1D1-B) | pValue_C1D1vsC2D1 | mean(C2D1-C1D1) | pValue_BvsC2D2 | mean(C2D1-B) | |
|---|---|---|---|---|---|---|
| B | 0.000 | -1.399 | 0.023 | -1.174 | 0.008 | -2.674 |
| cDC1 | 0.479 | -0.078 | 0.109 | 0.712 | 0.250 | 0.894 |
| cDC2 | 0.000 | -0.263 | 0.844 | -0.059 | 0.109 | -0.436 |
| DNT | 0.008 | -0.247 | 0.547 | -0.157 | 0.109 | -0.235 |
| Early Myelocyte | 0.001 | -1.085 | 0.844 | 0.703 | 0.383 | -0.112 |
| Granulocytes | 0.937 | -0.006 | 0.109 | -0.007 | 0.078 | -0.004 |
| Non-Classical Mono | 0.264 | -0.394 | 0.844 | 0.746 | 0.742 | -0.324 |
| pDC | 0.000 | -0.461 | 0.547 | 0.122 | 0.547 | -0.152 |
| preDC/Classical Mono | 0.007 | 8.032 | 0.313 | 6.048 | 0.016 | 16.117 |
| Tc | 0.662 | -0.525 | 0.023 | -2.823 | 0.008 | -2.930 |
| Th | 0.090 | -3.574 | 0.250 | -4.110 | 0.008 | -10.144 |
## [1] "Significant change (p-value < 0.05) in proportions of cells in the following cell types:"
## $pValue_BvsC1D1
## [1] "B" "cDC2" "DNT"
## [4] "Early Myelocyte" "pDC" "preDC/Classical Mono"
##
## $pValue_C1D1vsC2D1
## [1] "B" "Tc"
##
## $pValue_BvsC2D2
## [1] "B" "preDC/Classical Mono" "Tc"
## [4] "Th"
For significant cell types only
## [1] "The number of pairs (cluster, marker) with significant change (p-value < 0.05) in marker expression between baseline and C1D1:"
## [1] 152
## [1] "CD19 in B"
## [1] "CD117 in B"
## [1] "CD11B in B"
## [1] "CD1C in B"
## [1] "CCR2 in B"
## [1] "CD123 in B"
## [1] "CLEC9A in B"
## [1] "CD11C in B"
## [1] "CD141 in B"
## [1] "CD80 in B"
## [1] "TLR4 in B"
## [1] "CD172AB in B"
## [1] "CD40 in B"
## [1] "CD206 in B"
## [1] "HLADR in B"
## [1] "CD68 in B"
## [1] "PDL1 in B"
## [1] "CD3 in cDC1"
## [1] "CD11B in cDC1"
## [1] "CD4 in cDC1"
## [1] "CD8 in cDC1"
## [1] "CXCR2 in cDC1"
## [1] "CD1C in cDC1"
## [1] "FCERI in cDC1"
## [1] "CCR5 in cDC1"
## [1] "CLEC9A in cDC1"
## [1] "CD11C in cDC1"
## [1] "TLR4 in cDC1"
## [1] "CD40 in cDC1"
## [1] "CD206 in cDC1"
## [1] "CD33 in cDC1"
## [1] "CD68 in cDC1"
## [1] "CD116 in cDC1"
## [1] "PDL1 in cDC1"
## [1] "CD135 in cDC1"
## [1] "CD117 in cDC2"
## [1] "CD11B in cDC2"
## [1] "CD4 in cDC2"
## [1] "CD14 in cDC2"
## [1] "FCERI in cDC2"
## [1] "CD103 in cDC2"
## [1] "CCR2 in cDC2"
## [1] "CD123 in cDC2"
## [1] "CCR5 in cDC2"
## [1] "CD11C in cDC2"
## [1] "TLR4 in cDC2"
## [1] "CD172AB in cDC2"
## [1] "CD40 in cDC2"
## [1] "PDL2 in cDC2"
## [1] "CCR7 in cDC2"
## [1] "CD206 in cDC2"
## [1] "HLADR in cDC2"
## [1] "CD68 in cDC2"
## [1] "CD15 in cDC2"
## [1] "PDL1 in cDC2"
## [1] "CD16 in cDC2"
## [1] "Arg1 in cDC2"
## [1] "CD8 in DNT"
## [1] "CD163 in DNT"
## [1] "CLEC9A in DNT"
## [1] "CD11C in DNT"
## [1] "CD172AB in DNT"
## [1] "PDL2 in DNT"
## [1] "CCR7 in DNT"
## [1] "HLADR in DNT"
## [1] "PDL1 in DNT"
## [1] "CD3 in Early Myelocyte"
## [1] "CD4 in Early Myelocyte"
## [1] "CD8 in Early Myelocyte"
## [1] "CXCR2 in Early Myelocyte"
## [1] "CD66B in Early Myelocyte"
## [1] "CCR2 in Early Myelocyte"
## [1] "CCR5 in Early Myelocyte"
## [1] "CD11C in Early Myelocyte"
## [1] "CD141 in Early Myelocyte"
## [1] "CD40 in Early Myelocyte"
## [1] "PDL1 in Early Myelocyte"
## [1] "CD135 in Early Myelocyte"
## [1] "CD16 in Early Myelocyte"
## [1] "CCR5 in Granulocytes"
## [1] "CXCR4 in Granulocytes"
## [1] "CD4 in Non-Classical Mono"
## [1] "CD8 in Non-Classical Mono"
## [1] "CD14 in Non-Classical Mono"
## [1] "CD1C in Non-Classical Mono"
## [1] "FCERI in Non-Classical Mono"
## [1] "CCR2 in Non-Classical Mono"
## [1] "CD123 in Non-Classical Mono"
## [1] "CCR5 in Non-Classical Mono"
## [1] "CLEC9A in Non-Classical Mono"
## [1] "CD11C in Non-Classical Mono"
## [1] "CD141 in Non-Classical Mono"
## [1] "CD80 in Non-Classical Mono"
## [1] "CCR7 in Non-Classical Mono"
## [1] "CD33 in Non-Classical Mono"
## [1] "CD68 in Non-Classical Mono"
## [1] "CD116 in Non-Classical Mono"
## [1] "PDL1 in Non-Classical Mono"
## [1] "CD135 in Non-Classical Mono"
## [1] "CD16 in Non-Classical Mono"
## [1] "Arg1 in Non-Classical Mono"
## [1] "CD19 in pDC"
## [1] "CD4 in pDC"
## [1] "CCR2 in pDC"
## [1] "CD123 in pDC"
## [1] "TLR4 in pDC"
## [1] "CD172AB in pDC"
## [1] "CD40 in pDC"
## [1] "CD206 in pDC"
## [1] "CD33 in pDC"
## [1] "CD16 in pDC"
## [1] "CD19 in preDC/Classical Mono"
## [1] "CD117 in preDC/Classical Mono"
## [1] "CD11B in preDC/Classical Mono"
## [1] "CD14 in preDC/Classical Mono"
## [1] "CD66B in preDC/Classical Mono"
## [1] "CCR5 in preDC/Classical Mono"
## [1] "CD11C in preDC/Classical Mono"
## [1] "TLR4 in preDC/Classical Mono"
## [1] "CD172AB in preDC/Classical Mono"
## [1] "CD40 in preDC/Classical Mono"
## [1] "PDL2 in preDC/Classical Mono"
## [1] "CD206 in preDC/Classical Mono"
## [1] "PDL1 in preDC/Classical Mono"
## [1] "Arg1 in preDC/Classical Mono"
## [1] "CD1C in Tc"
## [1] "CCR2 in Tc"
## [1] "CD123 in Tc"
## [1] "CCR5 in Tc"
## [1] "CD11C in Tc"
## [1] "CD80 in Tc"
## [1] "CD172AB in Tc"
## [1] "CD33 in Tc"
## [1] "HLADR in Tc"
## [1] "CD68 in Tc"
## [1] "CD15 in Tc"
## [1] "PDL1 in Tc"
## [1] "Arg1 in Tc"
## [1] "CD1C in Th"
## [1] "FCERI in Th"
## [1] "CCR2 in Th"
## [1] "CD123 in Th"
## [1] "CCR5 in Th"
## [1] "CD11C in Th"
## [1] "CD172AB in Th"
## [1] "CD33 in Th"
## [1] "HLADR in Th"
## [1] "CD15 in Th"
## [1] "CXCR4 in Th"
## [1] "CD116 in Th"
## [1] "PDL1 in Th"
## [1] "Arg1 in Th"
## [1] "CD19 in B"
## [1] "CD117 in B"
## [1] "CD11B in B"
## [1] "CD1C in B"
## [1] "CCR2 in B"
## [1] "CD123 in B"
## [1] "CLEC9A in B"
## [1] "CD11C in B"
## [1] "CD141 in B"
## [1] "CD80 in B"
## [1] "TLR4 in B"
## [1] "CD172AB in B"
## [1] "CD40 in B"
## [1] "CD206 in B"
## [1] "HLADR in B"
## [1] "CD68 in B"
## [1] "PDL1 in B"
## [1] "CD3 in cDC1"
## [1] "CD11B in cDC1"
## [1] "CD4 in cDC1"
## [1] "CD8 in cDC1"
## [1] "CXCR2 in cDC1"
## [1] "CD1C in cDC1"
## [1] "FCERI in cDC1"
## [1] "CCR5 in cDC1"
## [1] "CLEC9A in cDC1"
## [1] "CD11C in cDC1"
## [1] "TLR4 in cDC1"
## [1] "CD40 in cDC1"
## [1] "CD206 in cDC1"
## [1] "CD33 in cDC1"
## [1] "CD68 in cDC1"
## [1] "CD116 in cDC1"
## [1] "PDL1 in cDC1"
## [1] "CD135 in cDC1"
## [1] "CD117 in cDC2"
## [1] "CD11B in cDC2"
## [1] "CD4 in cDC2"
## [1] "CD14 in cDC2"
## [1] "FCERI in cDC2"
## [1] "CD103 in cDC2"
## [1] "CCR2 in cDC2"
## [1] "CD123 in cDC2"
## [1] "CCR5 in cDC2"
## [1] "CD11C in cDC2"
## [1] "TLR4 in cDC2"
## [1] "CD172AB in cDC2"
## [1] "CD40 in cDC2"
## [1] "PDL2 in cDC2"
## [1] "CCR7 in cDC2"
## [1] "CD206 in cDC2"
## [1] "HLADR in cDC2"
## [1] "CD68 in cDC2"
## [1] "CD15 in cDC2"
## [1] "PDL1 in cDC2"
## [1] "CD16 in cDC2"
## [1] "Arg1 in cDC2"
## [1] "CD8 in DNT"
## [1] "CD163 in DNT"
## [1] "CLEC9A in DNT"
## [1] "CD11C in DNT"
## [1] "CD172AB in DNT"
## [1] "PDL2 in DNT"
## [1] "CCR7 in DNT"
## [1] "HLADR in DNT"
## [1] "PDL1 in DNT"
## [1] "CD3 in Early Myelocyte"
## [1] "CD4 in Early Myelocyte"
## [1] "CD8 in Early Myelocyte"
## [1] "CXCR2 in Early Myelocyte"
## [1] "CD66B in Early Myelocyte"
## [1] "CCR2 in Early Myelocyte"
## [1] "CCR5 in Early Myelocyte"
## [1] "CD11C in Early Myelocyte"
## [1] "CD141 in Early Myelocyte"
## [1] "CD40 in Early Myelocyte"
## [1] "PDL1 in Early Myelocyte"
## [1] "CD135 in Early Myelocyte"
## [1] "CD16 in Early Myelocyte"
## [1] "CCR5 in Granulocytes"
## [1] "CXCR4 in Granulocytes"
## [1] "CD4 in Non-Classical Mono"
## [1] "CD8 in Non-Classical Mono"
## [1] "CD14 in Non-Classical Mono"
## [1] "CD1C in Non-Classical Mono"
## [1] "FCERI in Non-Classical Mono"
## [1] "CCR2 in Non-Classical Mono"
## [1] "CD123 in Non-Classical Mono"
## [1] "CCR5 in Non-Classical Mono"
## [1] "CLEC9A in Non-Classical Mono"
## [1] "CD11C in Non-Classical Mono"
## [1] "CD141 in Non-Classical Mono"
## [1] "CD80 in Non-Classical Mono"
## [1] "CCR7 in Non-Classical Mono"
## [1] "CD33 in Non-Classical Mono"
## [1] "CD68 in Non-Classical Mono"
## [1] "CD116 in Non-Classical Mono"
## [1] "PDL1 in Non-Classical Mono"
## [1] "CD135 in Non-Classical Mono"
## [1] "CD16 in Non-Classical Mono"
## [1] "Arg1 in Non-Classical Mono"
## [1] "CD19 in pDC"
## [1] "CD4 in pDC"
## [1] "CCR2 in pDC"
## [1] "CD123 in pDC"
## [1] "TLR4 in pDC"
## [1] "CD172AB in pDC"
## [1] "CD40 in pDC"
## [1] "CD206 in pDC"
## [1] "CD33 in pDC"
## [1] "CD16 in pDC"
## [1] "CD19 in preDC/Classical Mono"
## [1] "CD117 in preDC/Classical Mono"
## [1] "CD11B in preDC/Classical Mono"
## [1] "CD14 in preDC/Classical Mono"
## [1] "CD66B in preDC/Classical Mono"
## [1] "CCR5 in preDC/Classical Mono"
## [1] "CD11C in preDC/Classical Mono"
## [1] "TLR4 in preDC/Classical Mono"
## [1] "CD172AB in preDC/Classical Mono"
## [1] "CD40 in preDC/Classical Mono"
## [1] "PDL2 in preDC/Classical Mono"
## [1] "CD206 in preDC/Classical Mono"
## [1] "PDL1 in preDC/Classical Mono"
## [1] "Arg1 in preDC/Classical Mono"
## [1] "CD1C in Tc"
## [1] "CCR2 in Tc"
## [1] "CD123 in Tc"
## [1] "CCR5 in Tc"
## [1] "CD11C in Tc"
## [1] "CD80 in Tc"
## [1] "CD172AB in Tc"
## [1] "CD33 in Tc"
## [1] "HLADR in Tc"
## [1] "CD68 in Tc"
## [1] "CD15 in Tc"
## [1] "PDL1 in Tc"
## [1] "Arg1 in Tc"
## [1] "CD1C in Th"
## [1] "FCERI in Th"
## [1] "CCR2 in Th"
## [1] "CD123 in Th"
## [1] "CCR5 in Th"
## [1] "CD11C in Th"
## [1] "CD172AB in Th"
## [1] "CD33 in Th"
## [1] "HLADR in Th"
## [1] "CD15 in Th"
## [1] "CXCR4 in Th"
## [1] "CD116 in Th"
## [1] "PDL1 in Th"
## [1] "Arg1 in Th"
## R version 4.3.2 (2023-10-31 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19045)
##
## Matrix products: default
##
##
## locale:
## [1] LC_COLLATE=English_United States.utf8
## [2] LC_CTYPE=English_United States.utf8
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.utf8
##
## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] grid stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] Matrix_1.6-3 data.table_1.14.8
## [3] BiocManager_1.30.22 survival_3.5-7
## [5] binom_1.1-1.1 flextable_0.9.4
## [7] survminer_0.4.9 msigdbr_7.5.1
## [9] fgsea_1.26.0 EnhancedVolcano_1.18.0
## [11] ComplexHeatmap_2.16.0 DESeq2_1.40.2
## [13] SummarizedExperiment_1.30.2 Biobase_2.60.0
## [15] MatrixGenerics_1.12.3 matrixStats_1.1.0
## [17] GenomicRanges_1.52.1 GenomeInfoDb_1.36.4
## [19] IRanges_2.34.1 S4Vectors_0.38.2
## [21] BiocGenerics_0.46.0 kableExtra_1.3.4
## [23] pals_1.8 gridExtra_2.3
## [25] DT_0.30 ggrepel_0.9.4
## [27] ggpubr_0.6.0 ggplot2_3.4.4
## [29] dplyr_1.1.2 knitr_1.45
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 rstudioapi_0.15.0 jsonlite_1.8.7
## [4] shape_1.4.6 magrittr_2.0.3 farver_2.1.1
## [7] rmarkdown_2.25 ragg_1.2.6 GlobalOptions_0.1.2
## [10] zlibbioc_1.46.0 vctrs_0.6.3 RCurl_1.98-1.13
## [13] askpass_1.2.0 rstatix_0.7.2 webshot_0.5.5
## [16] htmltools_0.5.7 S4Arrays_1.0.6 curl_5.1.0
## [19] broom_1.0.5 sass_0.4.8 bslib_0.6.1
## [22] htmlwidgets_1.6.4 plyr_1.8.9 cachem_1.0.8
## [25] zoo_1.8-12 uuid_1.1-1 mime_0.12
## [28] lifecycle_1.0.4 iterators_1.0.14 pkgconfig_2.0.3
## [31] R6_2.5.1 fastmap_1.1.1 GenomeInfoDbData_1.2.10
## [34] shiny_1.8.0 clue_0.3-65 digest_0.6.33
## [37] colorspace_2.1-0 crosstalk_1.2.1 textshaping_0.3.7
## [40] labeling_0.4.3 fansi_1.0.4 km.ci_0.5-6
## [43] httr_1.4.7 abind_1.4-5 compiler_4.3.2
## [46] fontquiver_0.2.1 withr_2.5.2 doParallel_1.0.17
## [49] backports_1.4.1 BiocParallel_1.34.2 carData_3.0-5
## [52] highr_0.10 maps_3.4.1.1 ggsignif_0.6.4
## [55] openssl_2.1.1 DelayedArray_0.26.7 rjson_0.2.21
## [58] gfonts_0.2.0 tools_4.3.2 zip_2.3.0
## [61] httpuv_1.6.12 glue_1.6.2 promises_1.2.1
## [64] reshape2_1.4.4 cluster_2.1.4 generics_0.1.3
## [67] gtable_0.3.4 KMsurv_0.1-5 tidyr_1.3.0
## [70] xml2_1.3.5 car_3.1-2 utf8_1.2.3
## [73] XVector_0.40.0 foreach_1.5.2 pillar_1.9.0
## [76] stringr_1.5.1 babelgene_22.9 later_1.3.1
## [79] circlize_0.4.15 splines_4.3.2 lattice_0.21-9
## [82] tidyselect_1.2.0 fontLiberation_0.1.0 locfit_1.5-9.8
## [85] fontBitstreamVera_0.1.1 svglite_2.1.2 crul_1.4.0
## [88] xfun_0.39 stringi_1.8.1 yaml_2.3.7
## [91] evaluate_0.23 codetools_0.2-19 httpcode_0.3.0
## [94] officer_0.6.3 gdtools_0.3.4 tibble_3.2.1
## [97] cli_3.6.1 xtable_1.8-4 systemfonts_1.0.5
## [100] jquerylib_0.1.4 munsell_0.5.0 survMisc_0.5.6
## [103] dichromat_2.0-0.1 Rcpp_1.0.11 mapproj_1.2.11
## [106] png_0.1-8 parallel_4.3.2 ellipsis_0.3.2
## [109] bitops_1.0-7 viridisLite_0.4.2 scales_1.3.0
## [112] purrr_1.0.2 crayon_1.5.2 GetoptLong_1.0.5
## [115] rlang_1.1.1 cowplot_1.1.2 fastmatch_1.1-4
## [118] rvest_1.0.3